How can I correct the degrees of freedom for any constraints? I used all
the whole trajectory to calculate Cp for the entire system, with the
original .edr files and using .edr files calculated using gmx energy and
notice the difference mentioned before.
I notice that for the same frame, the bond and potential energies are
different using the 2 methods, causing the difference in enthalpy and Cp.
I am seeking a solution to calculate Cp for the systems for which I do not
have the original .edr files. Please can you suggest any?
Thanks,
Malvika
On Fri, Feb 2, 2018 at 8:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> On 2/2/18 7:10 AM, Malvika K wrote:
>>> I have another query.
>>>> I have a protein in water system simulated at different temperatures and I
>> wish to calculate the heat capacity of the system. Unfortunately, at some
>> temperatures, I do not have the original .edr files.
>> In search of a way around this problem, I am wondering if I can use mdrun
>> -rerun to calculate the energies, extract the enthalpy and calculate Cp
>> using a script.
>> I checked this possibility for a temperature at which I do have the
>> original edr files. The Cp calculated by gromacs is 120.3 J/mol K. I also
>> used mdrun -rerun for the whole system and extracted enthalpy from the
>> output file.
>> The Cp calculated by the script is 82.2 J/mol K. I noticed that the
>> enthalpy values in the 2 files are quite different : -504693.187500 kJ/mol
>> (original edr) and -532618.500000 kJ/mol (via mdrun -rerun option).
>> The bond, potential/total energy values also differ in the 2 log files.
>>>> In this case, what would you suggest?
>>>> You need to correct the degrees of freedom for any constraints used, and
> also realize that .edr files contain full energy history so the values
> produced and corresponding statistics will be different from any quantity
> you try to recompute from only a subset of the frames in the system.
>> -Justin
>> --
> ==================================================
>> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>>jalemkul at vt.edu | (540) 231-3129
>http://www.biochem.vt.edu/people/faculty/JustinLemkul.html>> ==================================================
>>> --
> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/Support> /Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists>> * For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.>